nubos-pilot 0.5.5 → 0.5.7

package/agents/np-planner.md

@@ -223,13 +223,15 @@ Inside each `S<NNN>-PLAN.md`, every `<task>` tag MUST have these four attributes
 
 The scaffolder (`_extractTasksFromSlicePlan` in `bin/np-tools/plan-milestone.cjs`) reads ONLY these opening-tag attributes. Without them, zero task files are scaffolded and execute-phase has nothing to dispatch.
 
+Inside the body, every `<task>` MUST also contain a `<files_modified>` block listing the files the executor will touch (one per line or comma-separated). An empty or missing `<files_modified>` block produces `files_modified: []` in task frontmatter, which causes `commit-task` to fail (`commit-task-no-files`) unless the executor reported touched files via `checkpoint touch` as a runtime fallback. Plans MUST declare intent up-front; relying on the checkpoint fallback is a last-resort safety net.
+
 Correct example for `slices/S001/S001-PLAN.md`:
 
 ```
 <tasks>
 <task id="M001-S001-T0001" depends_on="" wave="1" tier="sonnet">
   <name>Seed login form</name>
-  <files>src/auth/LoginForm.tsx</files>
+  <files_modified>src/auth/LoginForm.tsx</files_modified>
   <read_first>
     - src/auth/AuthProvider.tsx
   </read_first>

package/bin/np-tools/commit-task.cjs

@@ -7,7 +7,7 @@ const { TASK_ID_RE, setTaskStatus } = require('../../lib/tasks.cjs');
 const layout = require('../../lib/layout.cjs');
 const git = require('../../lib/git.cjs');
 const { commitTask, findCommitByTaskId } = git;
-const { deleteCheckpoint } = require('../../lib/checkpoint.cjs');
+const { deleteCheckpoint, readCheckpoint } = require('../../lib/checkpoint.cjs');
 
 function _resolveTaskFile(taskId, cwd) {
   const parsed = layout.parseTaskFullId(taskId);
@@ -70,11 +70,21 @@ function run(args, ctx) {
   const { filePath } = _resolveTaskFile(taskId, cwd);
   const raw = fs.readFileSync(filePath, 'utf-8');
   const { frontmatter, body } = extractFrontmatter(raw);
-  const files = Array.isArray(frontmatter.files_modified) ? frontmatter.files_modified : [];
+  const declared = Array.isArray(frontmatter.files_modified) ? frontmatter.files_modified : [];
+  let files = declared.slice();
+  let filesSource = 'frontmatter';
+  if (files.length === 0) {
+    const cp = readCheckpoint(taskId, cwd);
+    const touched = cp && Array.isArray(cp.files_touched) ? cp.files_touched : [];
+    if (touched.length > 0) {
+      files = touched.slice();
+      filesSource = 'checkpoint';
+    }
+  }
   if (files.length === 0) {
     throw new NubosPilotError(
       'commit-task-no-files',
-      'Task ' + taskId + ' has empty files_modified',
+      'Task ' + taskId + ' has empty files_modified and no files_touched in checkpoint',
       { taskId },
     );
   }
@@ -93,7 +103,7 @@ function run(args, ctx) {
     process.stderr.write('[nubos-pilot warn] setTaskStatus failed for ' + taskId + ': ' + (err && err.message) + '\n');
   }
 
-  const payload = { ok: true, task_id: taskId, sha, files: safeFiles };
+  const payload = { ok: true, task_id: taskId, sha, files: safeFiles, files_source: filesSource };
   stdout.write(JSON.stringify(payload));
   return payload;
 }

package/bin/np-tools/commit-task.test.cjs

@@ -158,3 +158,40 @@ test('CT-5: commit-task unknown task id → task-not-found', () => {
     (err) => err && err.code === 'commit-task-not-found',
   );
 });
+
+test('CT-6: empty files_modified falls back to checkpoint.files_touched', () => {
+  const root = makeRepo();
+  seedPlanAndTask(root, '06-01', 'M006-S001-T0010', []);
+  fs.mkdirSync(path.join(root, 'src'), { recursive: true });
+  fs.writeFileSync(path.join(root, 'src', 'b.ts'), 'export const b = 2;\n', 'utf-8');
+  const cpPath = path.join(root, '.nubos-pilot', 'checkpoints', 'M006-S001-T0010.json');
+  fs.mkdirSync(path.dirname(cpPath), { recursive: true });
+  fs.writeFileSync(cpPath, JSON.stringify({
+    schema_version: 1,
+    task_id: 'M006-S001-T0010',
+    status: 'pre-commit',
+    files_touched: ['src/b.ts'],
+  }), 'utf-8');
+  const prev = process.cwd();
+  process.chdir(root);
+  const cap = _capture();
+  try {
+    subcmd.run(['M006-S001-T0010'], { cwd: root, stdout: cap.stub });
+  } finally {
+    process.chdir(prev);
+  }
+  const payload = JSON.parse(cap.get());
+  assert.equal(payload.ok, true);
+  assert.equal(payload.files_source, 'checkpoint');
+  assert.deepEqual(payload.files, ['src/b.ts']);
+});
+
+test('CT-7: empty files_modified AND no checkpoint → commit-task-no-files', () => {
+  const root = makeRepo();
+  seedPlanAndTask(root, '06-01', 'M006-S001-T0011', []);
+  const cap = _capture();
+  assert.throws(
+    () => subcmd.run(['M006-S001-T0011'], { cwd: root, stdout: cap.stub }),
+    (err) => err && err.code === 'commit-task-no-files',
+  );
+});

package/bin/np-tools/execute-milestone.cjs

@@ -8,6 +8,7 @@ const crypto = require('node:crypto');
 const {
   NubosPilotError,
   projectStateDir,
+  atomicWriteFileSync,
 } = require('../../lib/core.cjs');
 const layout = require('../../lib/layout.cjs');
 const { getPhase } = require('../../lib/roadmap.cjs');
@@ -141,6 +142,84 @@ function _initPayload(mNum, cwd) {
   };
 }
 
+function _readTaskSummaryBody(summaryPath) {
+  if (!fs.existsSync(summaryPath)) return null;
+  const raw = fs.readFileSync(summaryPath, 'utf-8');
+  const { body } = extractFrontmatter(raw);
+  return String(body || '').trim();
+}
+
+function _finalizeSlice(mNum, sNum, cwd) {
+  const slicePath = layout.findSliceDir(mNum, sNum, cwd);
+  if (!slicePath) {
+    throw new NubosPilotError(
+      'finalize-slice-not-found',
+      'Slice ' + layout.sliceFullId(mNum, sNum) + ' does not exist',
+      { milestone: mNum, slice: sNum },
+    );
+  }
+  const summaryPath = layout.sliceSummaryPath(mNum, sNum, cwd);
+  const tasks = _sliceTasksSorted(mNum, sNum, cwd);
+  const doneTasks = tasks.filter((t) => t.status === 'done');
+  const pendingTasks = tasks.filter((t) => t.status !== 'done');
+
+  const lines = [
+    '---',
+    'slice: ' + JSON.stringify(layout.sliceFullId(mNum, sNum)),
+    'milestone: ' + JSON.stringify(layout.mId(mNum)),
+    'type: slice-summary',
+    'task_count: ' + tasks.length,
+    'tasks_done: ' + doneTasks.length,
+    'tasks_pending: ' + pendingTasks.length,
+    'generated_at: ' + JSON.stringify(new Date().toISOString()),
+    '---',
+    '',
+    '# ' + layout.sliceFullId(mNum, sNum) + ' — SUMMARY',
+    '',
+    '_Auto-aggregated from task summaries by `execute-milestone finalize-slice`._',
+    '',
+    '## Task Roll-Up',
+    '',
+    '| Task | Status | Name |',
+    '|------|--------|------|',
+  ];
+  for (const t of tasks) {
+    lines.push('| ' + t.id + ' | ' + t.status + ' | ' + (t.name || '').replace(/\|/g, '\\|') + ' |');
+  }
+  lines.push('', '## Task Summaries', '');
+  for (const t of tasks) {
+    lines.push('### ' + t.id + ' — ' + (t.name || ''));
+    lines.push('');
+    const body = _readTaskSummaryBody(t.summary_path);
+    if (body) {
+      lines.push(body);
+    } else {
+      lines.push('_No T<NNNN>-SUMMARY.md file present._');
+    }
+    lines.push('');
+  }
+  atomicWriteFileSync(summaryPath, lines.join('\n'));
+  return {
+    slice: layout.sliceFullId(mNum, sNum),
+    summary_path: summaryPath,
+    task_count: tasks.length,
+    tasks_done: doneTasks.length,
+    tasks_pending: pendingTasks.length,
+  };
+}
+
+function _finalizeMilestone(mNum, cwd) {
+  const slices = layout.listSlices(mNum, cwd);
+  if (slices.length === 0) {
+    return { milestone: layout.mId(mNum), finalized: [], reason: 'no-slices' };
+  }
+  const finalized = [];
+  for (const s of slices) {
+    finalized.push(_finalizeSlice(mNum, s.number, cwd));
+  }
+  return { milestone: layout.mId(mNum), finalized, reason: 'ok' };
+}
+
 function _findTaskByFullId(mNum, taskFullId, cwd) {
   let parsed;
   try {
@@ -218,6 +297,19 @@ function run(args, ctx) {
       _emit(payload, stdout, cwd);
       return payload;
     }
+    case 'finalize-slice': {
+      const mNum = _validateMilestoneArg(list[1]);
+      const sNum = _validateMilestoneArg(list[2]);
+      const payload = _finalizeSlice(mNum, sNum, cwd);
+      _emit(payload, stdout, cwd);
+      return payload;
+    }
+    case 'finalize-milestone': {
+      const mNum = _validateMilestoneArg(list[1]);
+      const payload = _finalizeMilestone(mNum, cwd);
+      _emit(payload, stdout, cwd);
+      return payload;
+    }
     default:
       throw new NubosPilotError(
         'execute-milestone-unknown-verb',

package/bin/np-tools/execute-milestone.test.cjs

@@ -152,3 +152,98 @@ test('EM-6: unknown verb throws', () => {
     (err) => err && err.code === 'execute-milestone-unknown-verb',
   );
 });
+
+function _writeTaskSummary(sandbox, mNum, sNum, tNum, body) {
+  const mId = 'M' + String(mNum).padStart(3, '0');
+  const sId = 'S' + String(sNum).padStart(3, '0');
+  const tId = 'T' + String(tNum).padStart(4, '0');
+  const fullId = mId + '-' + sId + '-' + tId;
+  const dir = path.join(sandbox, '.nubos-pilot', 'milestones', mId, 'slices', sId, 'tasks', tId);
+  const content = [
+    '---',
+    'id: ' + JSON.stringify(fullId),
+    'status: done',
+    '---',
+    '',
+    body,
+    '',
+  ].join('\n');
+  fs.writeFileSync(path.join(dir, tId + '-SUMMARY.md'), content);
+}
+
+test('EM-7: finalize-slice writes S<NNN>-SUMMARY.md aggregating task summaries', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  seedSliceDir(sandbox, 1, 1, {});
+  _seedTask(sandbox, 1, 1, 1, ['src/a.ts']);
+  _seedTask(sandbox, 1, 1, 2, ['src/b.ts']);
+  _writeTaskSummary(sandbox, 1, 1, 1, '## Changes\n- Added src/a.ts');
+  _writeTaskSummary(sandbox, 1, 1, 2, '## Changes\n- Added src/b.ts');
+
+  const cap = _capture();
+  subcmd.run(['finalize-slice', '1', '1'], { cwd: sandbox, stdout: cap.stub });
+  const out = JSON.parse(cap.get());
+  assert.equal(out.slice, 'M001-S001');
+  assert.equal(out.task_count, 2);
+
+  const summaryPath = path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S001', 'S001-SUMMARY.md');
+  assert.ok(fs.existsSync(summaryPath));
+  const body = fs.readFileSync(summaryPath, 'utf-8');
+  assert.match(body, /slice: "M001-S001"/);
+  assert.match(body, /type: slice-summary/);
+  assert.match(body, /### M001-S001-T0001/);
+  assert.match(body, /### M001-S001-T0002/);
+  assert.match(body, /Added src\/a.ts/);
+  assert.match(body, /Added src\/b.ts/);
+});
+
+test('EM-8: finalize-slice fails when slice directory does not exist', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  const cap = _capture();
+  assert.throws(
+    () => subcmd.run(['finalize-slice', '1', '9'], { cwd: sandbox, stdout: cap.stub }),
+    (err) => err && err.code === 'finalize-slice-not-found',
+  );
+});
+
+test('EM-9: finalize-milestone iterates every slice and produces one summary per slice', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  seedSliceDir(sandbox, 1, 1, {});
+  seedSliceDir(sandbox, 1, 2, {});
+  _seedTask(sandbox, 1, 1, 1, ['src/a.ts']);
+  _seedTask(sandbox, 1, 2, 1, ['src/c.ts']);
+
+  const cap = _capture();
+  subcmd.run(['finalize-milestone', '1'], { cwd: sandbox, stdout: cap.stub });
+  const out = JSON.parse(cap.get());
+  assert.equal(out.milestone, 'M001');
+  assert.equal(out.finalized.length, 2);
+  assert.equal(out.reason, 'ok');
+
+  const s1 = path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S001', 'S001-SUMMARY.md');
+  const s2 = path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S002', 'S002-SUMMARY.md');
+  assert.ok(fs.existsSync(s1));
+  assert.ok(fs.existsSync(s2));
+});
+
+test('EM-10: finalize-slice marks tasks without SUMMARY.md but does not fail', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  seedSliceDir(sandbox, 1, 1, {});
+  _seedTask(sandbox, 1, 1, 1, ['src/a.ts']);
+  const dir = path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S001', 'tasks', 'T0001');
+  fs.rmSync(path.join(dir, 'T0001-SUMMARY.md'));
+
+  const cap = _capture();
+  subcmd.run(['finalize-slice', '1', '1'], { cwd: sandbox, stdout: cap.stub });
+  const out = JSON.parse(cap.get());
+  assert.equal(out.task_count, 1);
+  const body = fs.readFileSync(out.summary_path, 'utf-8');
+  assert.match(body, /No T<NNNN>-SUMMARY.md file present/);
+});

package/bin/np-tools/plan-milestone.cjs

@@ -163,12 +163,65 @@ function _extractTasksFromSlicePlan(planPath) {
   return out;
 }
 
+function _escapeRegex(s) {
+  return String(s).replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+}
+
+function _buildMilestoneRemap(mNum, cwd) {
+  const slices = layout.listSlices(mNum, cwd);
+  const remap = new Map();
+  for (const s of slices) {
+    const planPath = layout.slicePlanPath(mNum, s.number, cwd);
+    if (!fs.existsSync(planPath)) continue;
+    const tasks = _extractTasksFromSlicePlan(planPath);
+    tasks.forEach((t, idx) => {
+      const oldId = t.id;
+      if (!oldId) return;
+      const newId = layout.taskFullId(mNum, s.number, idx + 1);
+      if (oldId !== newId) remap.set(oldId, newId);
+    });
+  }
+  return remap;
+}
+
+function _rewriteSlicePlanIds(planPath, remap) {
+  if (remap.size === 0) return false;
+  const raw = fs.readFileSync(planPath, 'utf-8');
+  const keys = [...remap.keys()].sort((a, b) => b.length - a.length);
+  const re = new RegExp('\\b(' + keys.map(_escapeRegex).join('|') + ')\\b', 'g');
+  const next = raw.replace(re, (m) => remap.get(m) || m);
+  if (next === raw) return false;
+  atomicWriteFileSync(planPath, next);
+  return true;
+}
+
+function _normalizeMilestoneTaskIds(mNum, cwd) {
+  const remap = _buildMilestoneRemap(mNum, cwd);
+  if (remap.size === 0) return { changed: false, remap: {} };
+  const slices = layout.listSlices(mNum, cwd);
+  for (const s of slices) {
+    const planPath = layout.slicePlanPath(mNum, s.number, cwd);
+    if (!fs.existsSync(planPath)) continue;
+    _rewriteSlicePlanIds(planPath, remap);
+  }
+  return { changed: true, remap: Object.fromEntries(remap) };
+}
+
 function _extractInnerTag(body, tag) {
   const re = new RegExp('<' + tag + '(?:\\s[^>]*)?>([\\s\\S]*?)</' + tag + '>', 'i');
   const m = body.match(re);
   return m ? m[1].trim() : '';
 }
 
+function _parseFilesList(body) {
+  const raw = _extractInnerTag(body, 'files_modified') || _extractInnerTag(body, 'files');
+  if (!raw) return [];
+  return raw
+    .split(/[,\n]/)
+    .map((s) => s.trim().replace(/^[-*]\s+/, '').trim())
+    .filter(Boolean);
+}
+
 function _filesYaml(files) {
   if (!files.length) return '[]';
   return '\n' + files.map((f) => '  - ' + JSON.stringify(f)).join('\n');
@@ -184,8 +237,7 @@ function _renderTaskPlanMd(task, mNum, sNum) {
   const parsed = fullId.match(/T(\d{4,})$/);
   const taskNum = parsed ? Number(parsed[1]) : 0;
   const name = _extractInnerTag(task.body, 'name') || fullId;
-  const files = _extractInnerTag(task.body, 'files');
-  const filesList = files ? files.split(/[,\n]/).map((s) => s.trim()).filter(Boolean) : [];
+  const filesList = _parseFilesList(task.body);
   const readFirst = _extractInnerTag(task.body, 'read_first');
   const action = _extractInnerTag(task.body, 'action');
   const verify = _extractInnerTag(task.body, 'verify');
@@ -258,6 +310,13 @@ function _scaffoldSliceTasks(mNum, sNum, cwd) {
   if (!fs.existsSync(planPath)) {
     return { scaffolded: [], reason: 'no-slice-plan', slice: layout.sliceFullId(mNum, sNum) };
   }
+  const sliceRemap = new Map();
+  const preTasks = _extractTasksFromSlicePlan(planPath);
+  preTasks.forEach((t, idx) => {
+    const newId = layout.taskFullId(mNum, sNum, idx + 1);
+    if (t.id && t.id !== newId) sliceRemap.set(t.id, newId);
+  });
+  _rewriteSlicePlanIds(planPath, sliceRemap);
   const tasks = _extractTasksFromSlicePlan(planPath);
   if (tasks.length === 0) {
     return { scaffolded: [], reason: 'no-tasks-in-slice-plan', slice: layout.sliceFullId(mNum, sNum) };
@@ -293,12 +352,19 @@ function _scaffoldAllTasks(mNum, cwd) {
   if (slices.length === 0) {
     return { scaffolded: [], reason: 'no-slices', milestone: layout.mId(mNum) };
   }
+  const normalized = _normalizeMilestoneTaskIds(mNum, cwd);
   const per = [];
   for (const s of slices) {
     per.push(_scaffoldSliceTasks(mNum, s.number, cwd));
   }
   const total = per.reduce((acc, p) => acc + (p.task_count || 0), 0);
-  return { scaffolded: per, reason: 'ok', milestone: layout.mId(mNum), total_tasks: total };
+  return {
+    scaffolded: per,
+    reason: 'ok',
+    milestone: layout.mId(mNum),
+    total_tasks: total,
+    normalized_ids: normalized.changed ? normalized.remap : {},
+  };
 }
 
 function _createMilestoneDir(mNum, cwd) {

package/bin/np-tools/plan-milestone.test.cjs

@@ -207,3 +207,149 @@ test('PM-9: unknown verb throws', () => {
     (err) => err && err.code === 'plan-milestone-unknown-verb',
   );
 });
+
+test('PM-10: scaffold-all-tasks renumbers task ids per slice when planner numbered globally', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  const plan1 = [
+    '---', 'slice: "M001-S001"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S001-T0001" wave="1" tier="sonnet" depends_on=""><name>A</name><action>A</action><done>D</done></task>',
+    '<task id="M001-S001-T0002" wave="1" tier="sonnet" depends_on=""><name>B</name><action>A</action><done>D</done></task>',
+    '<task id="M001-S001-T0003" wave="1" tier="sonnet" depends_on=""><name>C</name><action>A</action><done>D</done></task>',
+  ].join('\n');
+  const plan2 = [
+    '---', 'slice: "M001-S002"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S002-T0004" wave="2" tier="sonnet" depends_on="M001-S001-T0003"><name>D</name><action>A</action><done>D</done></task>',
+    '<task id="M001-S002-T0005" wave="2" tier="sonnet" depends_on=""><name>E</name><action>A</action><done>D</done></task>',
+  ].join('\n');
+  const plan3 = [
+    '---', 'slice: "M001-S003"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S003-T0006" wave="3" tier="sonnet" depends_on="M001-S002-T0004"><name>F</name><action>A</action><done>D</done></task>',
+    '<task id="M001-S003-T0007" wave="3" tier="sonnet" depends_on="M001-S002-T0005,M001-S001-T0001"><name>G</name><action>A</action><done>D</done></task>',
+  ].join('\n');
+  seedSliceDir(sandbox, 1, 1, { 'S001-PLAN.md': plan1 });
+  seedSliceDir(sandbox, 1, 2, { 'S002-PLAN.md': plan2 });
+  seedSliceDir(sandbox, 1, 3, { 'S003-PLAN.md': plan3 });
+
+  const cap = _capture();
+  subcmd.run(['scaffold-all-tasks', '1'], { cwd: sandbox, stdout: cap.stub });
+  const out = JSON.parse(cap.get().trim());
+  assert.equal(out.reason, 'ok');
+  assert.equal(out.total_tasks, 7);
+
+  const tasksBase = path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices');
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S001', 'tasks', 'T0001')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S001', 'tasks', 'T0002')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S001', 'tasks', 'T0003')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S002', 'tasks', 'T0001')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S002', 'tasks', 'T0002')));
+  assert.ok(!fs.existsSync(path.join(tasksBase, 'S002', 'tasks', 'T0004')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S003', 'tasks', 'T0001')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'S003', 'tasks', 'T0002')));
+  assert.ok(!fs.existsSync(path.join(tasksBase, 'S003', 'tasks', 'T0006')));
+
+  const s2t1 = fs.readFileSync(path.join(tasksBase, 'S002', 'tasks', 'T0001', 'T0001-PLAN.md'), 'utf-8');
+  assert.match(s2t1, /id: "M001-S002-T0001"/);
+  assert.match(s2t1, /- "M001-S001-T0003"/);
+
+  const s3t1 = fs.readFileSync(path.join(tasksBase, 'S003', 'tasks', 'T0001', 'T0001-PLAN.md'), 'utf-8');
+  assert.match(s3t1, /id: "M001-S003-T0001"/);
+  assert.match(s3t1, /- "M001-S002-T0001"/);
+
+  const s3t2 = fs.readFileSync(path.join(tasksBase, 'S003', 'tasks', 'T0002', 'T0002-PLAN.md'), 'utf-8');
+  assert.match(s3t2, /id: "M001-S003-T0002"/);
+  assert.match(s3t2, /- "M001-S002-T0002"/);
+  assert.match(s3t2, /- "M001-S001-T0001"/);
+
+  const s2PlanRaw = fs.readFileSync(path.join(tasksBase, 'S002', 'S002-PLAN.md'), 'utf-8');
+  assert.match(s2PlanRaw, /id="M001-S002-T0001"/);
+  assert.match(s2PlanRaw, /id="M001-S002-T0002"/);
+  assert.doesNotMatch(s2PlanRaw, /T0004/);
+  assert.doesNotMatch(s2PlanRaw, /T0005/);
+
+  assert.deepEqual(out.normalized_ids['M001-S002-T0004'], 'M001-S002-T0001');
+  assert.deepEqual(out.normalized_ids['M001-S002-T0005'], 'M001-S002-T0002');
+  assert.deepEqual(out.normalized_ids['M001-S003-T0006'], 'M001-S003-T0001');
+  assert.deepEqual(out.normalized_ids['M001-S003-T0007'], 'M001-S003-T0002');
+});
+
+test('PM-11: scaffold-all-tasks is idempotent — already-normalized ids stay unchanged', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  const plan1 = [
+    '---', 'slice: "M001-S001"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S001-T0001" wave="1" tier="sonnet" depends_on=""><name>A</name><action>A</action><done>D</done></task>',
+  ].join('\n');
+  const plan2 = [
+    '---', 'slice: "M001-S002"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S002-T0001" wave="2" tier="sonnet" depends_on="M001-S001-T0001"><name>B</name><action>A</action><done>D</done></task>',
+  ].join('\n');
+  seedSliceDir(sandbox, 1, 1, { 'S001-PLAN.md': plan1 });
+  seedSliceDir(sandbox, 1, 2, { 'S002-PLAN.md': plan2 });
+
+  subcmd.run(['scaffold-all-tasks', '1'], { cwd: sandbox, stdout: _capture().stub });
+  const cap = _capture();
+  subcmd.run(['scaffold-all-tasks', '1'], { cwd: sandbox, stdout: cap.stub });
+  const out = JSON.parse(cap.get().trim());
+  assert.deepEqual(out.normalized_ids, {});
+});
+
+test('PM-13: scaffold accepts <files_modified> tag and strips bullet prefixes', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  const slicePlan = [
+    '---', 'slice: "M001-S001"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S001-T0001" wave="1" tier="sonnet" depends_on="">',
+    '  <name>Multi-file task</name>',
+    '  <files_modified>',
+    '    - src/a.ts',
+    '    - src/b.ts',
+    '    - src/c.ts',
+    '  </files_modified>',
+    '  <action>Touch three files.</action>',
+    '  <done>Done.</done>',
+    '</task>',
+  ].join('\n');
+  seedSliceDir(sandbox, 1, 1, { 'S001-PLAN.md': slicePlan });
+  subcmd.run(['scaffold-slice-tasks', '1', '1'], { cwd: sandbox, stdout: _capture().stub });
+  const body = fs.readFileSync(
+    path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S001', 'tasks', 'T0001', 'T0001-PLAN.md'),
+    'utf-8',
+  );
+  assert.match(body, /- "src\/a.ts"/);
+  assert.match(body, /- "src\/b.ts"/);
+  assert.match(body, /- "src\/c.ts"/);
+  assert.doesNotMatch(body, /- "- /);
+});
+
+test('PM-12: scaffold-slice-tasks renumbers its own slice when ids do not start at T0001', () => {
+  const sandbox = makeSandbox();
+  seedRoadmapYaml(sandbox, _roadmap());
+  seedMilestoneDir(sandbox, 1, {});
+  const plan2 = [
+    '---', 'slice: "M001-S002"', 'milestone: "M001"', '---', '',
+    '<task id="M001-S002-T0004" wave="2" tier="sonnet" depends_on=""><name>A</name><action>A</action><done>D</done></task>',
+    '<task id="M001-S002-T0005" wave="2" tier="sonnet" depends_on=""><name>B</name><action>A</action><done>D</done></task>',
+  ].join('\n');
+  seedSliceDir(sandbox, 1, 2, { 'S002-PLAN.md': plan2 });
+
+  const cap = _capture();
+  subcmd.run(['scaffold-slice-tasks', '1', '2'], { cwd: sandbox, stdout: cap.stub });
+  const out = JSON.parse(cap.get().trim());
+  assert.equal(out.task_count, 2);
+
+  const tasksBase = path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S002', 'tasks');
+  assert.ok(fs.existsSync(path.join(tasksBase, 'T0001')));
+  assert.ok(fs.existsSync(path.join(tasksBase, 'T0002')));
+  assert.ok(!fs.existsSync(path.join(tasksBase, 'T0004')));
+
+  const planRaw = fs.readFileSync(
+    path.join(sandbox, '.nubos-pilot', 'milestones', 'M001', 'slices', 'S002', 'S002-PLAN.md'),
+    'utf-8',
+  );
+  assert.match(planRaw, /id="M001-S002-T0001"/);
+  assert.doesNotMatch(planRaw, /T0004/);
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nubos-pilot",
-  "version": "0.5.5",
+  "version": "0.5.7",
   "description": "AI-driven planning and execution tool for code projects",
   "homepage": "https://github.com/Nubos-AI/nubos-pilot",
   "repository": {

package/workflows/execute-phase.md

@@ -136,7 +136,16 @@ for WAVE_INDEX in 0 1 2 ...; do
     fi
   done
   # wait for all parallel executors in this wave to finish before next wave
+
+  # After every task in the slice committed: aggregate per-task summaries into
+  # the slice-level S<NNN>-SUMMARY.md so /np:validate-phase can audit it.
+  SLICE_NUM=$(echo "$WAVE" | node -e "process.stdin.on('data', d => console.log(JSON.parse(d).wave))")
+  node .nubos-pilot/bin/np-tools.cjs init execute-milestone finalize-slice "$PHASE" "$SLICE_NUM" >/dev/null
 done
+
+# Milestone done — regenerate every slice summary so retroactive / resumed
+# runs also end with a complete audit surface.
+node .nubos-pilot/bin/np-tools.cjs init execute-milestone finalize-milestone "$PHASE" >/dev/null
 ```
 
 After every slice completes, point the operator at `/np:validate-phase $PHASE` to run the UAT per slice.